A new study published this month at Nature Genetics confirms with a direct measurement, multiple lines of evidence suggesting that mutation rates in modern humans are about half what had been assumed based on a presumed human-chimpanzee divergence date by most of the last decade's genetics papers. This factor of two difference is sufficient to make almost every interesting conclusion about pre-history that could be drawn from genetic data using the old dates wrong.
More intriguingly, it also suggests that about 85% of new mutations come from fathers, rather than mothers. While it has long been known that advanced paternal age is associated with new disease causing mutations, and the likely culprits behind this discrepancy have been identified, the general bias towards mutations having a paternal rather than a maternal source has been less widely appreciated.
The key line of the paper states: "we obtained an SNV mutation rate of 1.20 × 10−8 (95% confidence interval 0.89–1.43 × 10−8) mutations per base pair per generation. . . . there was strong evidence (P = 2.67 × 10−4) for a paternal bias in the origin of new mutations (85% paternal)."
For most of the genome, this gender bias isn't very important when trying to determine the age of a mutation. Everyone has a mother and a father. Everyone gets about half of their autosomal genome from each parent. So, gender differences in mutation rates all average out.
But, this may indicate that the proper mutation rate to use when determining the actual historic date when a mutation arose based on mutations observed in non-recombining Y-DNA may be higher than it is when attempting to estimate a historic date based upon mutations in autosomal DNA. Likewise, the mutation rates for autosomal X chromosomes may be somewhat lower than for autosomal DNA generally, because a disproportionate share of its lineage, although not 100% as in mtDNA, is from mother to child transmissions that are less mutation prone.
The difference in mutation rates in father to child genetic transmission as opposed to mother to daughter transmission could also adds to our understanding of the apparent discrepancies between the age of the root of the Y-DNA tree and estimates of the historic era of the most recent common ancestor of modern humans based on other population genetic methods (although this seems to make the problem worse rather than better).